Chapter 3 : Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era

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In light of the age of genomics, a compilation of small-subunit rRNA-encoding genes (16S rRNA genes) from is provided, with a phylogeny estimated from a subset of the sequences that spans the diversity of . Robust phylogeny estimation based on whole-genome sequences supports the close relationship of with another lineage of facultative intracellular bacteria, . The first genome sequence from the also reveals reductive genome evolution, with a genome size of 1.3 Mb and 1,195 predicted open reading frames (ORFs). Significant reclassification of the species within the was proposed based on data. Subsequent reevaluation of the trace file archives determined that the sequences discovered in were an artifact; however, 2,291 novel Wolbachia sequences were found in another fly genome, Drosophila willistoni. This work underscores the utility of eukaryotic genomes for discovering Rickettsiales endosymbionts and potentially assembling partial to complete bacterial genomes from the eukaryotic reads. A robust phylogeny based on whole-genome sequences supports the current taxonomic delineations within the and , with monophyly of each of the six genera strongly supported. The differences between RefSeq and Pathosystems Resource Integration Center (PATRIC) annotation undoubtedly result in discrepancies in protein family clustering between this work and previous studies. Two mitochondrial small-subunit rRNA gene sequences were included in the phylogeny estimation, and this lineage branched after the Holosporaceae, but basal to the derived Rickettsiales. The diversity of the highlighted in this chapter presents an exciting challenge for rickettsiology.

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3

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Bacterial Proteins
Mobile Genetic Elements
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Image of FIGURE 1

Compilation of genome statistics for 46 taxa. Taxon codes are described in Fig. 2 , with circles defining the monophyly of the major lineages: S, SAR11 clade; O, ; R, ; N, ; W, ; E, ; A, . Statistics for the outgroup taxa are not provided. Tree is a cladogram representation of the phylogram shown in Fig. 2 . RefSeq data were taken from GenBank, with statistics from PATRIC provided based on the RAST automated annotation technology ( ). Pl, plasmid; HP, hypothetical protein; FA, functional annotation. doi:10.1128/9781555817336.ch3.f1

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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Image of FIGURE 2

Whole-genome-based phylogeny estimation for 46 taxa. Taxon codes used in Fig. 1 are shown in parentheses after each organism name. The following pipeline was implemented to estimate phylogeny. BLAT (refined BLAST algorithm) ( ) searches were performed to identify similar protein sequences between all genomes, including the two outgroup taxa. To predict initial homologous protein sets, MCL ( ) was used to cluster BLAT results, with subsequent refinement of these sets using in-house hidden Markov models ( ). These protein families were then filtered to include only those with membership in >80% of the analyzed genomes (39 or more taxa included per protein family). Multiple sequence alignment of each protein family was performed using MUSCLE (default parameters) ( ), with masking of regions of poor alignment (length heterogeneous regions) done using Gblocks (default parameters) ( ). All modified alignments were then concatenated into one dataset. Tree building was performed using FastTree ( ). Support for generated lineages was estimated using a modified bootstrapping procedure, with 100 pseudoreplications sampling only half of the aligned protein sets per replication. (Note: Standard bootstrapping tends to produce inflated support values for very large alignments.) All branches in the illustrated tree were supported by 100%. Local refinements to tree topology were attempted in instances where highly supported nodes have subnodes with low support. This refinement is executed by running the entire pipeline on only those genomes represented by the node being refined (with additional sister taxa for rooting purposes). The refined subtree was then spliced back into the full tree. More information pertaining to this phylogeny pipeline is available at PATRIC. doi:10.1128/9781555817336.ch3.f2

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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Image of FIGURE 3a

Genus-level alignments of complete genome sequences. (A) Sixteen genomes: Br, RML369-C; Bo, OSU 85-389; Ca, McKiel; Ty, Wilmington; Pr, Madrid E; P2, Rp22; Fe, URRWXCal2; Ak, Hartford; Is, REIS; Ma, MTU5; Pe, Rustic; Ri, Sheila Smith; Rw, Iowa; Co, Malish 7; Si, 246; Af, ESF-5. (B) Two genomes: Bg, Boryong; Ik, Ikeda. (C) Two genomes: Rs, Illinois; Se, Miyayama. (D) Four genomes: Bm, endosymbiont strain TRS of ; Me, symbiont of . ; Wr, endosymbiont sp. Ri; Qp, symbiont of Pel. (E) Five genomes: Cj, Jake; Ha, Arkansas; Re, Welgevonden (Erwe); Ro, Welgevonden (Erum); Rg, Gardel. (F) Four genomes: Ce, Israel; Mf, Florida; Ms, St. Maries; Ph, HZ. Complete genome sequences were downloaded from PATRIC ( ). Alignments constructed with MAUVE (progressive) v. 2.3.1 ( ). Numbers above each alignment depict genome coordinates in Mb. doi:10.1128/9781555817336.ch3.f3

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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Image of FIGURE 3b

Genus-level alignments of complete genome sequences. (A) Sixteen genomes: Br, RML369-C; Bo, OSU 85-389; Ca, McKiel; Ty, Wilmington; Pr, Madrid E; P2, Rp22; Fe, URRWXCal2; Ak, Hartford; Is, REIS; Ma, MTU5; Pe, Rustic; Ri, Sheila Smith; Rw, Iowa; Co, Malish 7; Si, 246; Af, ESF-5. (B) Two genomes: Bg, Boryong; Ik, Ikeda. (C) Two genomes: Rs, Illinois; Se, Miyayama. (D) Four genomes: Bm, endosymbiont strain TRS of ; Me, symbiont of . ; Wr, endosymbiont sp. Ri; Qp, symbiont of Pel. (E) Five genomes: Cj, Jake; Ha, Arkansas; Re, Welgevonden (Erwe); Ro, Welgevonden (Erum); Rg, Gardel. (F) Four genomes: Ce, Israel; Mf, Florida; Ms, St. Maries; Ph, HZ. Complete genome sequences were downloaded from PATRIC ( ). Alignments constructed with MAUVE (progressive) v. 2.3.1 ( ). Numbers above each alignment depict genome coordinates in Mb. doi:10.1128/9781555817336.ch3.f3

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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Image of FIGURE 4

Comparative analysis of select genome sequences. (A) Heat map representation of the distribution of proteins across 12 selected genomes. (Note: For six genera, the two most divergent and complete genomes were selected.) O, genomes: Bg, Boryong; Ik, Ikeda. R, genomes: Br, RML369-C; Ty, Wilmington. N, genomes: Rs, Illinois; Se, Miyayama. W, genomes: Bm, endosymbiont strain TRS of ; Wr, endosymbiont sp. Ri. A, genomes: Ms, St. Maries; Ph, HZ. E, genomes: Cj, Jake; Rg, Gardel. Black depicts no representative proteins per genome, with shading spectrum (light to dark gray) illustrating one to multiple genes per genome. Heat map constructed using the Protein Family Sorter tool at PATRIC ( ). Protein families are based on curated subsystems (FIGFams), which form the core component of the RAST automated annotation technology ( ). (B) Schema depicting the protein families shared at the order, family, and genus levels. Unique proteins (singletons) are also listed for each genome. (C) Graphic representation of the membership of 1,858 protein families and 4,289 singletons. doi:0.1128/9781555817336.ch3.f4

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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Image of FIGURE 5

Genomic analysis of genes involved PG synthesis, transport, degradation, and recycling in . (A) PG pathway: brown, aminosugar metabolism; green, early-stage muropeptide synthesis; blue, lipid I and lipid II synthesis and translocation; red, anhydromuropeptide transpeptidation and transglycosylation; purple, PG degradation and turnover. Dashed pathway lines depict enzymes not encoded in any genome. (B) Distribution of PG-associated genes across select genomes. taxon codes are described in the Fig. 3 legend, except for Pu (“ Pelagibacter ubique” HTCC1062). Letters over cladogram: P, “ Pelagibacter,” , ; , ; , ; , ; , ; , . Open circles depict gene absence; closed circles, gene presence; numbers, multiple gene copies; S, split ORF. doi:10.1128/9781555817336.ch3.f5

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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Image of FIGURE 6

Phylogeny estimation of small-subunit rRNA gene sequences from 47 diverse taxa and 2 mitochondria. Sequences were aligned using MUSCLE v3.6 ( ) with default parameters, and subsequently analyzed under maximum likelihood using RAxML ( ). A gamma model of rate heterogeneity was used with estimation of the proportion of invariable sites. Brach support is from 1,000 bootstrap pseudoreplications. The term “” is used as originally suggested ( ). (Note: PATRIC accession numbers are given for rRNA gene sequences retrieved from completed genomes; all other numbers are NCBI nucleotide accession numbers.) Taxon information is as follows, moving from the top to the bottom of the tree. “ Pelagibacter ubique” HTCC1002 (VBICanPel113578_r025); alphaproteobacterium strain HIMB114 (VBIAlpPro140191_r032); uncultured bacterium clone PRTBB8516 (HM798949); “ Captivus acidiprotistae” (AF533508); uncultured “ Odyssella sp.” clone 5-F (EU305601); bacterium strain Serialkilleuse_9403403 (HM138368); “ Trojanella thessalonicensis” L13 (AF069496); endosymbiont of sp. KA/E23 (EF140636); 221 (X71837); “ Caedibacter acanthamoebae” (AF132138); “ Paraholospora nucleivisitans” (EU652696); uncultured bacterium clone Oh3123O11E (EU137369); (X58198); , mitochondria (NC_001660); , mitochondria (AF007261); “ Cryptoprodotis polytropus” isolate PSM1 (FM201293); “ Occidentia massiliensis” ( bacterium strain Os18; GU937608); Ikeda (VBIOriTsu129072_r006); secondary symbiont of clone Hefei (HM156647); uncultured bacterium clone SHFG464 (FJ203077); bacterial symbiont of (AJ630204); uncultured bacterium clone EV221H2111601SAH71 (DQ223223); endosymbiont of (AB066351); endosymbiont of (FM955311); RML369-C (VBIRicBel102610_r012); REIS (VBIRicEnd40569_r031); uncultured alphaproteobacterium clone SM1B06 (AF445655); “ Xenohaliotis californiensis” (AF069062); (U12457); Illinois (VBINeoRis104330_r001); uncultured sp. isolate 184 (EU780451); endosymbiont strain TRS of (VBIWolEnd7741_r015); endosymbiont of (M85267); “ Neoanaplasma japonica” ( bacterium strain IS136; AB190771); Gardel (VBIEhrRum72196_r011); “ Neoehrlichia mikurensis” (uncultured “ Neoehrlichia sp.” clone 2; GQ501090); St. Maries (VBIAnaMar46146_r010); (AY125087); uncultured bacterium clone Hv(lakePohlsee)_25 (EF667921); “ Cyrtobacter comes” (FN552697); uncultured bacterium “Montezuma” (AF493952); “ Anadelfobacter veles” (FN552695); uncultured alphaproteobacterium clone MD3.55 (FJ425643); uncultured proteobacterium clone PEACE2006/237_P3 (EU394580); uncultured bacterium clone Ho_lab_2_5 (EF667892); endosymbiont of sp. UWC36 (AF069962); uncultured bacterium clone ID25L (EU555284); “ Midichloria mitochondrii” (AJ566640); “ Nicolleia massiliensis” France (DQ788562). doi:10.1128/9781555817336.ch3.f6

Citation: Gillespie J, Nordberg E, Sobral B, Azad A. 2012. Phylogeny and Comparative Genomics: the Shifting Landscape in the Genomics Era, p 84-141. In Palmer G, Azad A (ed), Intracellular Pathogens II: . ASM Press, Washington, DC. doi: 10.1128/9781555817336.ch3
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1. Abamo, F.,, H. Dohra,, and M. Fujishima. 2008. Fate of the 63-kDa periplasmic protein of the infectious form of the endonuclear symbiotic bacterium Holospora obtusa during the infection process. FEMS Microbiol. Lett. 280:2127.PubMed CrossRef
2. Abergel, C.,, G. Blanc,, V. Monchois,, P. Renesto,, C. Sigoillot,, H. Ogata,, D. Raoult,, and J. M. Claverie. 2006. Impact of the excision of an ancient repeat insertion on Rickettsia conorii guanylate kinase activity. Mol. Biol. Evol. 23:21122122.PubMed CrossRef
3. Abhishek, A.,, A. Bavishi,, and M. Choudhary. 2011. Bacterial genome chimaerism and the origin of mitochondria. Can. J. Microbiol. 57:4961PubMed CrossRef
4. Agnes, J. T.,, K. A. Brayton,, M. LaFollett,, J. Norimine,, W. C. Brown,, and G. H. Palmer. 2011. Identification of Anaplasma marginale outer membrane protein antigens conserved between A. marginale sensu stricto strains and the live A. marginale subsp. centrale vaccine. Infect. Immun. 79:13111318.PubMed CrossRef
5. Alvarez-Martinez, C. E.,, and P. J. Christie. 2009. Biological diversity of prokaryotic type IV secretion systems. Microbiol. Mol. Biol. Rev. 73:775808.PubMed CrossRef
6. Amann, R. I.,, W. Ludwig,, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143169.PubMed
7. Amann, R.,, N. Springer,, W. Ludwig,, H. D. Görtz,, and K. H. Schleifer. 1991. Identification in situ and phylogeny of uncultured bacterial endosymbionts. Nature 351:161164.PubMed CrossRef
8. Amano, K.,, A. Tamura,, N. Ohashi,, H. Urakami,, S. Kaya,, and K. Fukushi. 1987. Deficiency of peptidoglycan and lipopolysaccharide components in Rickettsia tsutsugamushi. Infect. Immun. 55:22902292.PubMed
9. Amiri, H.,, C. M. Alsmark,, and S. G. Andersson. 2002. Proliferation and deterioration of Rickettsia Palindromic Elements. Mol. Biol. Evol. 19:12341243.PubMed
10. Andersson, J. O.,, and S. G. Andersson. 1999. Insights into the evolutionary process of genome degradation. Curr. Opin. Genet. Dev. 9:664671.PubMed
11. Andersson, S. G.,, A. S. Eriksson,, A. K. Naslund,, M. S. Andersen,, and C. G. Kurland. 1996. The Rickettsia prowazekii genome: a random sequence analysis. Microb. Comp. Genomics 1:293315.PubMed
12. Andersson, S. G.,, D. R. Stothard,, P. Fuerst,, and C. G. Kurland. 1999. Molecular phylogeny and rearrangement of rRNA genes in Rickettsia species. Mol. Biol. Evol. 16:987995.PubMed
13. Andersson, S. G.,, A. Zomorodipour,, J. O. Andersson,, T. Sicheritz-Pontén,, U. C. Alsmark,, R. M. Podowski,, A. K. Naslund,, A. S. Eriksson, H. H. Winkler, and C. G. Kurland. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133140.PubMed CrossRef
14. Andersson, S. G.,, A. Zomorodipour,, H. H. Winkler,, and C. G. Kurland. 1995. Unusual organization of the rRNA genes in Rickettsia prowazekii. J. Bacteriol. 177:41714175.PubMed
15. Antonio, D. B.,, K. B. Andree,, J. D. Moore,, C. S. Friedman,, and R. P. Hedrick. 2000. Detection of Rickettsiales-like prokaryotes by in situ hybridization in black abalone, Haliotis cracherodii, with withering syndrome. J. Invertebr. Pathol. 75:180182.PubMed CrossRef
16. Audia, J. P.,, and H. H. Winkler. 2006. Study of the five Rickettsia prowazekii proteins annotated as ATP/ADP translocases (Tlc): only Tlc1 transports ATP/ADP, while Tlc4 and Tlc5 transport other ribonucleotides. J. Bacteriol. 188:62616268.PubMed CrossRef
17. Azad, A. F. 2007. Pathogenic rickettsiae as bioterrorism agents. Clin. Infect. Dis. 45(Suppl. 1):S52S55.PubMed CrossRef
18. Azad, A. F.,, M. S. Beier,, and J. J. Gillespie,. 2008. The Rickettsiaceae, p. 439450. In L. Green, and E. Goldman (ed.), Practical Handbook of Microbiology. CRC Press, Boca Raton, FL.
19. Azad, A. F.,, and S. Radulovic. 2003. Pathogenic rickettsiae as bioterrorism agents. Ann. N. Y. Acad. Sci. 990:734738.PubMed CrossRef
20. Aziz, R. K.,, D. Bartels,, A. A. Best,, M. DeJongh,, T. Disz,, R. A. Edwards,, K. Formsma,, S. Gerdes,, E. M. Glass,, M. Kubal,, F. Meyer,, G. J. Olsen,, R. Olson,, A. L. Osterman,, R. A. Overbeek,, L. K. McNeil,, D. Paarmann,, T. Paczian,, B. Parrello,, G. D. Pusch,, C. Reich,, R. Stevens,, O. Vassieva,, V. Vonstein,, A. Wilke,, and O. Zagnitko. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75.PubMed CrossRef
21. Baker, B. J.,, P. Hugenholtz,, S. C. Dawson,, and J. F. Banfield. 2003. Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes. Appl. Environ. Microbiol. 69:55125518.PubMed
22. Balayeva, N. M.,, M. E. Eremeeva,, V. F. Ignatovich,, B. A. Dmitriev,, E. B. Lapina,, and L. S. Belousova. 1992. Protein antigens of genetically related Rickettsia prowazekii strains with different virulence. Acta Virol. 36:5256.PubMed
23. Balayeva, N. M.,, M. E. Eremeeva,, H. Tissot-Dupont,, I. A. Zakharov,, and D. Raoult. 1995. Genotype characterization of the bacterium expressing the male-killing trait in the ladybird beetle Adalia bipunctata with specific rickettsial molecular tools. Appl. Environ. Microbiol. 61:14311437.PubMed
24. Baldridge, G. D.,, N. Y. Burkhardt,, R. F. Felsheim,, T. J. Kurtti,, and U. G. Munderloh. 2007. Transposon insertion reveals pRM, a plasmid of Rickettsia monacensis. Appl. Environ. Microbiol. 73:49844995.PubMed CrossRef
25. Baldridge, G. D.,, N. Y. Burkhardt,, R. F. Felsheim,, T. J. Kurtti,, and U. G. Munderloh. 2008. Plasmids of the pRM/pRF family occur in diverse Rickettsia species. Appl. Environ. Microbiol. 74:645652.PubMed CrossRef
26. Baldridge, G. D.,, N. Y. Burkhardt,, M. B. Labruna,, R. C. Pacheco,, C. D. Paddock,, P. C. Williamson,, P. M. Billingsley,, R. F. Felsheim,, T. J. Kurtti,, and U. G. Munderloh. 2010. Wide dispersal and possible multiple origins of low-copy-number plasmids in Rickettsia species associated with blood-feeding arthropods. Appl. Environ. Microbiol. 76:17181731.PubMed CrossRef
27. Baldridge, G. D.,, N. Y. Burkhardt,, J. A. Simser,, T. J. Kurtti,, and U. G. Munderloh. 2004. Sequence and expression analysis of the ompA gene of Rickettsia peacockii, an endosymbiont of the Rocky Mountain wood tick, Dermacentor andersoni. Appl. Environ. Microbiol. 70:66286636.PubMed CrossRef
28. Balraj, P.,, K. El Karkouri,, G. Vestris,, L. Espinosa,, D. Raoult,, and P. Renesto. 2008. RickA expression is not sufficient to promote actin-based motility of Rickettsia raoultii. PLoS One 3:e2582.PubMed CrossRef
29. Bechah, Y.,, K. El Karkouri,, O. Mediannikov,, Q. Leroy,, N. Pelletier,, C. Robert,, C. Medigue,, J. L. Mege,, and D. Raoult. 2010. Genomic, proteomic, and transcriptomic analysis of virulent and avirulent Rickettsia prowazekii reveals its adaptive mutation capabilities. Genome Res. 20:655663.PubMed CrossRef
30. Beier, C. L.,, M. Horn,, R. Michel,, M. Schweikert,, H. D. Görtz,, and M. Wagner. 2002. The genus Caedibacter comprises endosymbionts of Paramecium spp. related to the Rickettsiales (Alphaproteobacteria) and to Francisella tularensis (Gammaproteobacteria). Appl. Environ. Microbiol. 68:60436050.PubMed
31. Beninati, T.,, N. Lo,, L. Sacchi,, C. Genchi,, H. Noda,, and C. Bandi. 2004. A novel alpha-proteobacterium resides in the mitochondria of ovarian cells of the tick Ixodes ricinus. Appl. Environ. Microbiol. 70:25962602.PubMed CrossRef
32. Beninati, T.,, M. Riegler,, I. M. Vilcins,, L. Sacchi,, R. McFadyen,, M. Krockenberger,, C. Bandi,, S. L. O’Neill,, and N. Lo. 2009. Absence of the symbiont Candidatus Midichloria mitochondrii in the mitochondria of the tick Ixodes holocyclus. FEMS Microbiol. Lett. 299:241247.PubMed CrossRef
33. Birtles, R. J.,, T. G. Harrison,, N. A. Saunders,, and D. H. Molyneux. 1995. Proposals to unify the genera Grahamella and Bartonella, with descriptions of Bartonella talpae comb. nov., Bartonella peromysci comb. nov., and three new species, Bartonella grahamii sp. nov., Bartonella taylorii sp. nov., and Bartonella doshiae sp. nov. Int. J. Syst. Bacteriol. 45:18.PubMed CrossRef
34. Birtles, R. J.,, T. J. Rowbotham,, R. Michel,, D. G. Pitcher,, B. Lascola,, S. Alexiou-Daniel,, and D. Raoult. 2000. Candidatus Odyssella thessalonicensis’ gen. nov., sp. nov., an obligate intracellular parasite of Acanthamoeba species. Int. J. Syst. Evol. Microbiol. 50:6372.PubMed CrossRef
35. Blanc, G.,, M. Ngwamidiba,, H. Ogata,, P. E. Fournier,, J. M. Claverie,, and D. Raoult. 2005. Molecular evolution of rickettsia surface antigens: evidence of positive selection. Mol. Biol. Evol. 22:20732083.PubMed CrossRef
36. Blanc, G.,, H. Ogata,, C. Robert,, S. Audic,, J. M. Claverie,, and D. Raoult. 2007a. Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome. Genome Res. 17:16571664.PubMed CrossRef
37. Blanc, G.,, H. Ogata,, C. Robert,, S. Audic,, K. Suhre,, G. Vestris,, J. M. Claverie,, and D. Raoult. 2007b. Reductive genome evolution from the mother of Rickettsia. PLoS Genet. 3:e14.PubMed CrossRef
38. Blaxter, M. 2007. Symbiont genes in host genomes: fragments with a future? Cell Host Microbe 2:211213.PubMed CrossRef
39. Bordenstein, S. R. 2007. Evolutionary genomics: transdomain gene transfers. Curr. Biol. 17:R935R936.PubMed CrossRef
40. Braid, B. A.,, J. D. Moore,, T. T. Robbins,, R. P. Hedrick,, R. S. Tjeerdema,, and C. S. Friedman. 2005. Health and survival of red abalone, Haliotis rufescens, under varying temperature, food supply, and exposure to the agent of withering syndrome. J. Invertebr. Pathol. 89:219231.PubMed CrossRef
41. Braig, H. R.,, B. D. Turner,, and M. A. Perotti,. 2008. Symbiotic rickettsia, p. 221249. In K. Bourtzis, and T. A. Miller (ed.), Insect Symbiosis, vol. 3. CRC Press, Boca Raton, FL.
42. Braig, H. R.,, W. Zhou,, S. L. Dobson,, and S. L. O’Neill. 1998. Cloning and characterization of a gene encoding the major surface protein of the bacterial endosymbiont Wolbachia pipientis. J. Bacteriol. 180:23732378.PubMed
43. Brayton, K. A.,, L. S. Kappmeyer,, D. R. Herndon,, M. J. Dark,, D. L. Tibbals,, G. H. Palmer,, T. C. McGuire,, and D. P. Knowles, Jr. 2005. Complete genome sequencing of Anaplasma marginale reveals that the surface is skewed to two superfamilies of outer membrane proteins. Proc. Natl. Acad. Sci. USA 102:844849.PubMed CrossRef
44. Brayton, K. A.,, D. P. Knowles,, T. C. McGuire,, and G. H. Palmer. 2001. Efficient use of a small genome to generate antigenic diversity in tick-borne ehrlichial pathogens. Proc. Natl. Acad. Sci. USA 98:41304135.PubMed CrossRef
45. Brayton, K. A.,, G. H. Palmer,, A. Lundgren,, J. Yi,, and A. F. Barbet. 2002. Antigenic variation of Anaplasma marginale msp2 occurs by combinatorial gene conversion. Mol. Microbiol. 43:11511159.PubMed CrossRef
46. Brenner, D. J.,, S. P. O’Connor,, H. H. Winkler,, and A. G. Steigerwalt. 1993. Proposals to unify the genera Bartonella and Rochalimaea, with descriptions of Bartonella quintana comb. nov., Bartonella vinsonii comb. nov., Bartonella henselae comb. nov., and Bartonella elizabethae comb. nov., and to remove the family Bartonellaceae from the order Rickettsiales. Int. J. Syst. Bacteriol. 43:777786.PubMed CrossRef
47. Brindefalk, B.,, T. J. Ettema,, J. Viklund,, M. Thollesson,, and S. G. Andersson. 2011. A phylometagenomic exploration of oceanic alphaproteobacteria reveals mitochondrial relatives unrelated to the SAR11 clade. PLoS One 6:e24457.PubMed CrossRef
48. Campbell, B. C.,, T. S. Bragg,, and C. E. Turner. 1992. Phylogeny of symbiotic bacteria of four weevil species (Coleoptera: Curculionidae) based on analysis of 16S ribosomal DNA. Insect Biochem. Mol. Biol. 22:415421.
49. Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540552.PubMed
50. Chafee, M. E.,, D. J. Funk,, R. G. Harrison,, and S. R. Bordenstein. 2010. Lateral phage transfer in obligate intracellular bacteria (Wolbachia): verification from natural populations. Mol. Biol. Evol. 27:501505.PubMed CrossRef
51. Chen, D. Q.,, B. C. Campbell,, and A. H. Purcell. 1996. A new rickettsia from a herbivorous insect, the pea aphid Acyrthosiphon pisum (Harris). Curr. Microbiol. 33:123128.PubMed CrossRef
52. Cho, N. H.,, H. R. Kim,, J. H. Lee,, S. Y. Kim,, J. Kim,, S. Cha,, A. C. Darby,, H. H. Fuxelius,, J. Yin,, J. H. Kim,, S. J. Lee,, Y. S. Koh,, W. J. Jang,, K. H. Park,, S. G. Andersson,, M. S. Choi,, and I. S. Kim. 2007. The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes. Proc. Natl. Acad. Sci. USA 104:79817986.PubMed CrossRef
53. Claverie, J. M.,, and H. Ogata. 2003. The insertion of palindromic repeats in the evolution of proteins. Trends Biochem. Sci. 28:7580.PubMed CrossRef
54. Collins, N. E.,, J. Liebenberg,, E. P. de Villiers,, K. A. Brayton,, E. Louw,, A. Pretorius,, F. E. Faber,, H. van Heerden,, A. Josemans,, M. van Kleef,, H. C. Steyn,, M. F. van Strijp,, E. Zweygarth,, F. Jongejan,, J. C. Maillard,, D. Berthier,, M. Botha,, F. Joubert,, C. H. Corton,, N. R. Thomson,, M. T. Allsopp,, and B. A. Allsopp. 2005. The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number. Proc. Natl. Acad. Sci. USA 102:838843.PubMed CrossRef
55. Dame, J. B.,, S. M. Mahan,, and C. A. Yowell. 1992. Phylogenetic relationship of Cowdria ruminantium, agent of heartwater, to Anaplasma marginale and other members of the order Rickettsiales determined on the basis of 16S rRNA sequence. Int. J. Syst. Bacteriol. 42:270274.PubMed CrossRef
56. Dandekar, T.,, S. Schuster,, B. Snel,, M. Huynen,, and P. Bork. 1999. Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem. J. 343:115124.PubMed
57. Darby, A. C.,, N. H. Cho,, H. H. Fuxelius,, J. Westberg,, and S. G. Andersson. 2007. Intracellular pathogens go extreme: genome evolution in the Rickettsiales. Trends Genet. 23:511520.PubMed CrossRef
58. Dark, M. J.,, B. Al-Khedery,, and A. F. Barbet. 2011. Multistrain genome analysis identifies candidate vaccine antigens of Anaplasma marginale. Vaccine 29:49234932.PubMed CrossRef
59. Dark, M. J.,, D. R. Herndon,, L. S. Kappmeyer,, M. P. Gonzales,, E. Nordeen,, G. H. Palmer,, D. P. Knowles, Jr.,, and K. A. Brayton. 2009. Conservation in the face of diversity: multistrain analysis of an intracellular bacterium. BMC Genomics 10:16.PubMed CrossRef
60. Darling, A. E.,, B. Mau,, and N. T. Perna. 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147.PubMed CrossRef
61. Daugherty, R. M.,, N. Linka,, J. P. Audia,, C. Urbany,, H. E. Neuhaus,, and H. H. Winkler. 2004. The nucleotide transporter of Caedibacter caryophilus exhibits an extended substrate spectrum compared to the analogous ATP/ADP translocase of Rickettsia prowazekii. J. Bacteriol. 186:32623265.PubMed
62. Davis, A. K.,, J. L. DeVore,, J. R. Milanovich,, K. Cecala,, J. C. Maerz,, and M. J. Yabsley. 2009. New findings from an old pathogen: intraerythrocytic bacteria (family Anaplasmatacea) in red-backed salamanders Plethodon cinereus. Ecohealth 6:219228.PubMed CrossRef
63. Davis, M. J.,, Z. Ying,, B. R. Brunner,, A. Pantoja,, and F. H. Ferwerda. 1998. Rickettsial relative associated with papaya bunchy top disease. Curr. Microbiol. 36:8084.PubMed CrossRef
64. Dohra, H.,, M. Fujishima,, and H. Ishikawa. 1998. Structure and expression of a GroE-homologous operon of a macronucleus-specific symbiont Holospora obtusa of the ciliate Paramecium caudatum. J. Eukaryot. Microbiol. 45:7179.PubMed
65. Dohra, H.,, K. Yamamoto,, M. Fujishima,, and H. Ishikawa. 1997. Cloning and sequencing of gene coding for a periplasmic 5.4 kDa peptide of the macronucleus-specific symbiont Holospora obtusa of the ciliate Paramecium caudatum. Zoolog. Sci. 14:6975.PubMed
66. Dong, X.,, K. El Karkouri,, C. Robert,, F. Gavory,, D. Raoult,, and P. E. Fournier. 2012. Genomic comparison of Rickettsia helvetica and other Rickettsia species. J. Bacteriol. 194:2751.PubMed CrossRef
67. Duan, C.,, Y. Tong,, Y. Huang,, X. Wang,, X. Xiong,, and B. Wen. 2011. Complete genome sequence of Rickettsia heilongjiangensis, an emerging tick-transmitted human pathogen. J. Bacteriol. 193:55645565.PubMed CrossRef
68. Dumler, J. S.,, A. F. Barbet,, C. P. Bekker,, G. A. Dasch,, G. H. Palmer,, S. C. Ray,, Y. Rikihisa,, and F. R. Rurangirwa. 2001. Reorganization of genera in the families Rickettsiaceae and Anaplasmataceae in the order Rickettsiales: unification of some species of Ehrlichia with Anaplasma, Cowdria with Ehrlichia and Ehrlichia with Neorickettsia, descriptions of six new species combinations and designation of Ehrlichia equi and ‘HGE agent’ as subjective synonyms of Ehrlichia phagocytophila. Int. J. Syst. Evol. Microbiol. 51:21452165.PubMed CrossRef
69. Dumler, J. S.,, and D. H. Walker,. 2005. Order II. Rickettsiales Gieszczykiewicz 1939, 25AL emend. Dumler, Barbet, Bekker, Dasch, Palmer, Ray, Rikihisa and Rurangirwa 2001, 2156, p. 96145. In G. M. Garrity,, D. J. Brenner,, N. R. Krieg,, and J. T. Staley (ed.), Bergey’s Manual of Systematic Bacteriology, 2nd ed., vol. 2. Springer-Verlag, New York, NY.
70. Dunning Hotopp, J. C.,, M. E. Clark,, D. C. Oliveira,, J. M. Foster,, P. Fischer,, M. C. Munoz Torres,, J. D. Giebel,, N. Kumar,, N. Ishmael,, S. Wang,, J. Ingram,, R. V. Nene,, J. Shepard,, J. Tomkins,, S. Richards,, D. J. Spiro,, E. Ghedin,, B. E. Slatko,, H. Tettelin,, and J. H. Werren. 2007. Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317:17531756.PubMed CrossRef
71. Dunning Hotopp, J. C.,, M. Lin,, R. Madupu,, J. Crabtree,, S. V. Angiuoli,, J. Eisen,, R. Seshadri,, Q. Ren,, M. Wu,, T. R. Utterback,, S. Smith,, M. Lewis,, H. Khouri,, C. Zhang,, H. Niu,, Q. Lin,, N. Ohashi,, N. Zhi,, W. Nelson,, L. M. Brinkac,, R. J. Dodson,, M. J. Rosovitz,, J. Sundaram,, S. C. Daugherty,, T. Davidsen,, A. S. Durkin,, M. Gwinn,, D. H. Haft,, J. D. Selengut,, S. A. Sullivan,, N. Zafar,, L. Zhou,, F. Benahmed,, H. Forberger,, R. Halpin,, S. Mulligan,, J. Robinson,, O. White,, Y. Rikihisa,, and H. Tettelin. 2006. Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet. 2:e21.PubMed CrossRef
72. Durbin, R.,, S. Eddy,, A. Krogh,, and G. Mitchison. 1998. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, United Kingdom.
73. Dwyer, D. S. 2001. Selfish DNA and the origin of genes. Science 291:252253.PubMed CrossRef
74. Edgar, R. C. 2004a. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113.PubMed CrossRef
75. Edgar, R. C. 2004b. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:17921797.PubMed CrossRef
76. Ellison, D. W.,, T. R. Clark,, D. E. Sturdevant,, K. Virtaneva,, S. F. Porcella,, and T. Hackstadt. 2008. Genomic comparison of virulent Rickettsia rickettsii Sheila Smith and avirulent Rickettsia rickettsii Iowa. Infect. Immun. 76:542550.PubMed CrossRef
77. Emelyanov, V. V. 2001a. Evolutionary relationship of Rickettsiae and mitochondria. FEBS Lett. 501:1118.PubMed
78. Emelyanov, V. V. 2001b. Rickettsiaceae, rickettsia-like endosymbionts, and the origin of mitochondria. Biosci. Rep. 21:117.PubMed
79. Emelyanov, V. V. 2003a. Common evolutionary origin of mitochondrial and rickettsial respiratory chains. Arch. Biochem. Biophys. 420:130141.PubMed
80. Emelyanov, V. V. 2003b. Mitochondrial connection to the origin of the eukaryotic cell. Eur. J. Biochem. 270:15991618.PubMed CrossRef
81. Emelyanov, V. V., 2007. Constantin Merezhkowsky and the Endokaryotic Hypothesis, p. 201237. In W. F. Martin, and M. Müller (ed.), Origin of Mitochondria and Hydrogenosomes. Springer-Verlag, Berlin, Heidelberg.
82. Emelyanov, V. V.,, and B. V. Sinitsyn,. 1999. A groE-based phylogenetic analysis shows the closest evolutionary relationship of mitochondria to obligate intracytoplasmic bacterium Rickettsia prowazekii, p. 3137. In D. Raoult, and P. Brouqui (ed.), Rickettsiae and Rickettsial Diseases at the Turn of the Third Millennium. Elsevier, Marseille, France.
83. Epis, S.,, D. Sassera,, T. Beninati,, N. Lo,, L. Beati,, J. Piesman,, L. Rinaldi,, K. D. McCoy,, A. Torina,, L. Sacchi,, E. Clementi,, M. Genchi,, S. Magnino,, and C. Bandi. 2008. Midichloria mitochondrii is widespread in hard ticks (Ixodidae) and resides in the mitochondria of phylogenetically diverse species. Parasitology 135:485494.PubMed CrossRef
84. Eremeeva, M. E.,, A. Madan,, C. D. Shaw,, K. Tang,, and G. A. Dasch. 2005. New perspectives on rickettsial evolution from new genome sequences of Rickettsia, particularly R. canadensis, and Orientia tsutsugamushi. Ann. N. Y. Acad. Sci. 1063:4763.PubMed CrossRef
85. Eschbach, E.,, M. Pfannkuchen,, M. Schweikert,, D. Drutschmann,, F. Brümmer,, S. Fokin,, W. Ludwig,, and H. D. Görtz. 2009. Candidatus Paraholospora nucleivisitans”, an intracellular bacterium in Paramecium sexaurelia shuttles between the cytoplasm and the nucleus of its host. Syst. Appl. Microbiol. 32:490500.PubMed CrossRef
86. Ettema, T. J.,, and S. G. Andersson. 2009. The α-proteobacteria: the Darwin finches of the bacterial world. Biol. Lett. 5:429432.PubMed CrossRef
87. Federici, B. A. 1980. Reproduction and morphogenesis of Rickettsiella chironomi, an unusual intracellular procaryotic parasite of midge larvae. J. Bacteriol. 143:9951002.PubMed
88. Fehr, J. S.,, G. V. Bloemberg,, C. Ritter,, M. Hombach,, T. F. Lüscher,, R. Weber,, and P. M. Keller. 2010. Septicemia caused by tick-borne bacterial pathogen Candidatus Neoehrlichia mikurensis. Emerg. Infect. Dis. 16:11271129.PubMed CrossRef
89. Felsheim, R. F.,, T. J. Kurtti,, and U. G. Munderloh. 2009. Genome sequence of the endosymbiont Rickettsia peacockii and comparison with virulent Rickettsia rickettsii: identification of virulence factors. PLoS One 4:e8361.PubMed CrossRef
90. Ferrantini, F.,, S. I. Fokin,, L. Modeo,, I. Andreoli,, F. Dini,, H. D. Görtz,, F. Verni,, and G. Petroni. 2009. Candidatus Cryptoprodotis polytropus,” a novel Rickettsia-like organism in the ciliated protist Pseudomicrothorax dubius (Ciliophora, Nassophorea). J. Eukaryot. Microbiol. 56:119129.PubMed CrossRef
91. Forsman, M.,, G. Sandström,, and A. Sjöstedt. 1994. Analysis of 16S ribosomal DNA sequences of Francisella strains and utilization for determination of the phylogeny of the genus and for identification of strains by PCR. Int. J. Syst. Bacteriol. 44:3846.PubMed CrossRef
92. Foster, J.,, M. Ganatra,, I. Kamal,, J. Ware,, K. Makarova,, N. Ivanova,, A. Bhattacharyya,, V. Kapatral,, S. Kumar,, J. Posfai,, T. Vincze,, J. Ingram,, L. Moran,, A. Lapidus,, M. Omelchenko,, N. Kyrpides,, E. Ghedin,, S. Wang,, E. Goltsman,, V. Joukov,, O. Ostrovskaya,, K. Tsukerman,, M. Mazur,, D. Comb,, E. Koonin,, and B. Slatko. 2005. The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol. 3:e121.PubMed CrossRef
93. Fournier, P. E.,, L. Belghazi,, C. Robert,, K. Elkarkouri,, A. L. Richards,, G. Greub,, F. Collyn,, M. Ogawa,, A. Portillo,, J. A. Oteo,, A. Psaroulaki,, I. Bitam,, and D. Raoult. 2008. Variations of plasmid content in Rickettsia felis. PLoS One 3:e2289.PubMed CrossRef
94. Fournier, P. E.,, K. El Karkouri,, Q. Leroy,, C. Robert,, B. Giumelli,, P. Renesto,, C. Socolovschi,, P. Parola,, S. Audic,, and D. Raoult. 2009. Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction. BMC Genomics 10:166.PubMed CrossRef
95. Fournier, P. E.,, K. El Karkouri,, C. Robert,, C. Medigue,, and D. Raoult. 2012. Complete genome sequence of Rickettsia slovaca, the agent of tick-borne lymphadenitis. J. Bacteriol. 194:1612.PubMed CrossRef
96. Fraune, S.,, and T. C. Bosch. 2007. Long-term maintenance of species-specific bacterial microbiota in the basal metazoan Hydra. Proc. Natl. Acad. Sci. USA 104:1314613151.PubMed CrossRef
97. Friedman, C. S.,, K. B. Andree,, K. A. Beauchamp,, J. D. Moore,, T. T. Robbins,, J. D. Shields,, and R. P. Hedrick. 2000. Candidatus Xenohaliotis californiensis’, a newly described pathogen of abalone, Haliotis spp., along the west coast of North America. Int. J. Syst. Evol. Microbiol. 50:847855.PubMed CrossRef
98. Fritsche, T. R.,, R. K. Gautom,, S. Seyedirashti,, D. L. Bergeron,, and T. D. Lindquist. 1993. Occurrence of bacterial endosymbionts in Acanthamoeba spp. isolated from corneal and environmental specimens and contact lenses. J. Clin. Microbiol. 31:11221126.PubMed
99. Fritsche, T. R.,, M. Horn,, S. Seyedirashti,, R. K. Gautom,, K. H. Schleifer,, and M. Wagner. 1999. In situ detection of novel bacterial endosymbionts of Acanthamoeba spp. phylogenetically related to members of the order Rickettsiales. Appl. Environ. Microbiol. 65:206212.PubMed
100. Frohlich, K. M.,, R. A. Roberts,, N. A. Housley,, and J. P. Audia. 2010. Rickettsia prowazekii uses an sn-glycerol-3-phosphate dehydrogenase and a novel dihydroxyacetone phosphate transport system to supply triose phosphate for phospholipid biosynthesis. J. Bacteriol. 192:42814288.PubMed CrossRef
101. Frutos, R.,, B. A. Federici,, B. Revet,, and M. Bergoin. 1994. Taxonomic studies of Rickettsiella, Rickettsia, and Chlamydia using genomic DNA. J. Invertebr. Pathol. 63:294300.PubMed CrossRef
102. Frutos, R.,, A. Viari,, C. Ferraz,, A. Morgat,, S. Eychenie,, Y. Kandassamy,, I. Chantal,, A. Bensaid,, E. Coissac,, N. Vachiery,, J. Demaille,, and D. Martinez. 2006. Comparative genomic analysis of three strains of Ehrlichia ruminantium reveals an active process of genome size plasticity. J. Bacteriol. 188:25332542.PubMed CrossRef
103. Fuxelius, H. H.,, A. C. Darby,, N. H. Cho,, and S. G. Andersson. 2008. Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction. Genome Biol. 9:R42.PubMed CrossRef
104. Fuxelius, H. H.,, A. Darby,, C. K. Min,, N. H. Cho,, and S. G. Andersson. 2007. The genomic and metabolic diversity of Rickettsia. Res. Microbiol. 158:745753.PubMed CrossRef
105. Gardner, G. R.,, J. C. Harshbarger,, J. L. Lake,, T. K. Sawyer,, K. L. Price,, M. D. Stephenson,, P. L. Haaker,, and H. A. Togstad. 1995. Association of prokaryotes with symptomatic appearance of withering syndrome in black abalone Haliotis cracherodii. J. Invertebr. Pathol. 66:111120.PubMed CrossRef
106. Gavotte, L.,, H. Henri,, R. Stouthamer,, D. Charif,, S. Charlat,, M. Boulétreau,, and F. Vavre. 2007. A Survey of the bacteriophage WO in the endosymbiotic bacteria Wolbachia. Mol. Biol. Evol. 24:427435.PubMed CrossRef
107. Ge, H.,, Y. Y. Chuang,, S. Zhao,, M. Tong,, M. H. Tsai,, J. J. Temenak,, A. L. Richards,, and W. M. Ching. 2004. Comparative genomics of Rickettsia prowazekii Madrid E and Breinl strains. J. Bacteriol. 186:556565.PubMed CrossRef
108. Georgiades, K.,, M. A. Madoui,, P. Le,, C. Robert,, and D. Raoult. 2011. Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion. PLoS One 6:e24857.PubMed CrossRef
109. Gillespie, J. J.,, N. C. Ammerman,, M. Beier-Sexton,, B. S. Sobral,, and A. F. Azad. 2009a. Louse- and flea-borne rickettsioses: biological and genomic analyses. Vet. Res. 40:12.PubMed CrossRef
110. Gillespie, J. J.,, N. C. Ammerman,, S. M. Dreher-Lesnick,, M. S. Rahman,, M. J. Worley,, J. C. Setubal,, B. S. Sobral,, and A. F. Azad. 2009b. An anomalous type IV secretion system in Rickettsia is evolutionarily conserved. PLoS One 4:e4833.PubMed CrossRef
111. Gillespie, J. J.,, M. S. Beier,, M. S. Rahman,, N. C. Ammerman,, J. M. Shallom,, A. Purkayastha,, B. S. Sobral,, and A. F. Azad. 2007. Plasmids and rickettsial evolution: insight from Rickettsia felis. PLoS One 2:e266.PubMed CrossRef
112. Gillespie, J. J.,, K. A. Brayton,, K. P. Williams,, M. A. Diaz,, W. C. Brown,, A. F. Azad,, and B. W. Sobral. 2010. Phylogenomics reveals a diverse Rickettsiales type IV secretion system. Infect. Immun. 78:18091823.PubMed CrossRef
113. Gillespie, J. J.,, V. Joardar,, K. P. Williams,, T. Driscoll,, J. B. Hostetler,, E. Nordberg,, M. Shukla,, B. Wallenz,, C. A. Hill,, V. M. Nene,, A. F. Azad,, B. W. Sobral,, and E. Caler. 4 November 2011a. A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of obligate intracellular lifestyle. J. Bacteriol. doi:10.1128/?JB.06244-11.PubMed CrossRef
114. Gillespie, J. J.,, A. R. Wattam,, S. A. Cammer,, J. L. Gabbard,, M. P. Shukla,, O. Dalay,, T. Driscoll,, D. Hix,, S. P. Mane,, C. Mao,, E. K. Nordberg,, M. Scott,, J. R. Schulman,, E. E. Snyder,, D. E. Sullivan,, C. Wang,, A. Warren,, K. P. Williams,, T. Xue,, H. S. Yoo,, C. Zhang,, Y. Zhang,, R. Will,, R. W. Kenyon,, and B. W. Sobral. 2011b. PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect. Immun. 79:42864298.PubMed CrossRef
115. Gillespie, J. J.,, K. Williams,, M. Shukla,, E. E. Snyder,, E. K. Nordberg,, S. M. Ceraul,, C. Dharmanolla,, D. Rainey,, J. Soneja,, J. M. Shallom,, N. D. Vishnubhat,, R. Wattam,, A. Purkayastha,, M. Czar,, O. Crasta,, J. C. Setubal,, A. F. Azad,, and B. S. Sobral. 2008. Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life. PLoS One 3:e2018.PubMed CrossRef
116. Giovannoni, S. J.,, H. J. Tripp,, S. Givan,, M. Podar,, K. L. Vergin,, D. Baptista,, L. Bibbs,, J. Eads,, T. H. Richardson,, M. Noordewier,, M. S. Rappe,, J. M. Short,, J. C. Carrington,, and E. J. Mathur. 2005. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309:12421245.PubMed CrossRef
117. Görtz, H. D.,, and M. Fujishima. 1983. Conjugation and meiosis of Paramecium caudatum infected with the micronucleus-specific bacterium Holospora elegans. Eur. J. Cell Biol. 32:8691.PubMed
118. Görtz, H. D.,, S. Lellig,, O. Miosga,, and M. Wiemann. 1990. Changes in fine structure and polypeptide pattern during development of Holospora obtusa, a bacterium infecting the macronucleus of Paramecium caudatum. J. Bacteriol. 172:56645669.PubMed
119. Görtz, H. D.,, and H. J. Schmidt,. 2005. Family III. Holosporaceae fam. nov., p. 146160. In G. M. Garrity,, D. J. Brenner,, N. R. Krieg,, and J. T. Staley (ed.), Bergey’s Manual of Systematic Bacteriology, 2nd ed., vol. 2. Springer-Verlag, New York, NY.
120. Götz, P. 1971. “Multiple cell division” as a mode of reproduction of a cell-parasitic bacterium. Naturwissenchaften 58:569570.PubMed
121. Götz, P. 1972. Rickettsiella chironomi”: an unusual bacterial pathogen which reproduces by multiple cell division. J. Invertebr. Pathol. 20:2230.PubMed
122. Gouin, E.,, C. Egile,, P. Dehoux,, V. Villiers,, J. Adams,, F. Gertler,, R. Li,, and P. Cossart. 2004. The RickA protein of Rickettsia conorii activates the Arp2/3 complex. Nature 427:457461.PubMed CrossRef
123. Gromov, B. V.,, and D. V. Ossipov. 1981. Holospora (ex Hafkine 1890) nom. rev., a genus of bacteria inhabiting the nuclei of paramecia. Int. J. Syst. Bacteriol. 31:348352.
124. Hackstadt, T. 1996. The biology of rickettsiae. Infect. Agents Dis. 5:127143.PubMed
125. Haglund, C. M.,, J. E. Choe,, C. T. Skau,, D. R. Kovar,, and M. D. Welch. 2010. Rickettsia Sca2 is a bacterial formin-like mediator of actin-based motility. Nat. Cell Biol. 12:10571063.PubMed CrossRef
126. Hall, J.,, and H. Voelz. 1985. Bacterial endosymbionts of Acanthamoeba sp. J. Parasitol. 71:8995.PubMed
127. Herndon, D. R.,, G. H. Palmer,, V. Shkap,, D. P. Knowles, Jr.,, and K. A. Brayton. 2010. Complete genome sequence of Anaplasma marginale subsp. centrale. J. Bacteriol. 192:379380.PubMed CrossRef
128. Hilgenboecker, K.,, P. Hammerstein,, P. Schlattmann,, A. Telschow,, and J. H. Werren. 2008. How many species are infected with Wolbachia?—a statistical analysis of current data. FEMS Microbiol. Lett. 281:215220.PubMed CrossRef
129. Hori, M.,, K. Fujii,, and M. Fujishima. 2008. Micronucleus-specific bacterium Holospora elegans irreversibly enhances stress gene expression of the host Paramecium caudatum. J. Eukaryot. Microbiol. 55:515521.PubMed CrossRef
130. Horn, M.,, T. R. Fritsche,, R. K. Gautom,, K. H. Schleifer,, and M. Wagner. 1999. Novel bacterial endosymbionts of Acanthamoeba spp. related to the Paramecium caudatum symbiont Caedibacter caryophilus. Environ. Microbiol. 1:357367.PubMed CrossRef
131. Inokuma, H.,, P. Brouqui,, M. Drancourt,, and D. Raoult. 2001. Citrate synthase gene sequence: a new tool for phylogenetic analysis and identification of Ehrlichia. J. Clin. Microbiol. 39:30313039.PubMed CrossRef
132. Ishmael, N.,, J. C. Dunning Hotopp,, P. Ioannidis,, S. Biber,, J. Sakamoto,, S. Siozios,, V. Nene,, J. Werren,, K. Bourtzis,, S. R. Bordenstein,, and H. Tettelin. 2009. Extensive genomic diversity of closely related Wolbachia strains. Microbiology 155:22112222.PubMed CrossRef
133. Iwatani, K.,, H. Dohra,, B. F. Lang,, G. Burger,, M. Hori,, and M. Fujishima. 2005. Translocation of an 89-kDa periplasmic protein is associated with Holospora infection. Biochem. Biophys. Res. Commun. 337:11981205.PubMed CrossRef
134. Jeng, R. L.,, E. D. Goley,, J. A. D’Alessio,, O. Y. Chaga,, T. M. Svitkina,, G. G. Borisy,, R. A. Heinzen,, and M. D. Welch. 2004. A Rickettsia WASP-like protein activates the Arp2/3 complex and mediates actin-based motility. Cell. Microbiol. 6:761769.PubMed CrossRef
135. Jones, R. T.,, K. F. McCormick,, and A. P. Martin. 2008. Bacterial communities of Bartonella-positive fleas: diversity and community assembly patterns. Appl. Environ. Microbiol. 74:16671670.PubMed CrossRef
136. Kent, B. N.,, L. Salichos,, J. G. Gibbons,, A. Rokas,, I. L. Newton,, M. E. Clark,, and S. R. Bordenstein. 2011. Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture. Genome Biol. Evol. 3:209218.PubMed CrossRef
137. Kent, W. J. 2002. BLAT—the BLAST-like alignment tool. Genome Res. 12:656664.PubMed CrossRef
138. Kikuchi, Y.,, S. Sameshima,, O. Kitade, J. Kojima, and T. Fukatsu. 2002. Novel clade of Rickettsia spp. from leeches. Appl. Environ. Microbiol. 68:9991004.PubMed
139. Klasson, L.,, Z. Kambris,, P. E. Cook,, T. Walker,, and S. P. Sinkins. 2009a. Horizontal gene transfer between Wolbachia and the mosquito Aedes aegypti. BMC Genomics 10:33.PubMed CrossRef
140. Klasson, L.,, T. Walker,, M. Sebaihia,, M. J. Sanders,, M. A. Quail,, A. Lord,, S. Sanders,, J. Earl,, S. L. O’Neill,, N. Thomson,, S. P. Sinkins,, and J. Parkhill. 2008. Genome evolution of Wolbachia strain wPip from the Culex pipiens group. Mol. Biol. Evol. 25:18771887.PubMed CrossRef
141. Klasson, L.,, J. Westberg,, P. Sapountzis,, K. Naslund,, Y. Lutnaes,, A. C. Darby,, Z. Veneti,, L. Chen,, H. R. Braig,, R. Garrett,, K. Bourtzis,, and S. G. Andersson. 2009b. The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans. Proc. Natl. Acad. Sci. USA 106:57255730.PubMed CrossRef
142. Kuchler, S. M.,, S. Kehl,, and K. Dettner. 2009. Characterization and localization of Rickettsia sp. in water beetles of genus Deronectes (Coleoptera: Dytiscidae). FEMS Microbiol. Ecol. 68:201211.PubMed CrossRef
143. Kurland, C. G.,, and S. G. Andersson. 2000. Origin and evolution of the mitochondrial proteome. Microbiol. Mol. Biol. Rev. 64:786820.PubMed
144. Kusch, J.,, and H. D. Görtz. 2006. Towards an understanding of the killer trait: Caedibacter endocytobionts in Paramecium. Prog. Mol. Subcell. Biol. 41:6176.PubMed
145. Kusch, J.,, M. Stremmel,, H. W. Breiner,, V. Adams,, M. Schweikert,, and H. J. Schmidt. 2000. The toxic symbiont Caedibacter caryophila in the cytoplasm of Paramecium novaurelia. Microb. Ecol. 40:330335.PubMed CrossRef
146. Lang, B. F.,, H. Brinkmann,, L. B. Koski,, M. Fujishima,, H. D. Görtz,, and G. Burger. 2005. On the origin of mitochondria and Rickettsia-related eukaryotic endosymbionts. Jpn. J. Protozool. 38:171183.
147. Li, T.,, J. H. Xiao,, Z. H. Xu,, R. W. Murphy,, and D. W. Huang. 2011. A possibly new Rickettsia-like genus symbiont is found in Chinese wheat pest aphid, Sitobion miscanthi (Hemiptera: Aphididae). J. Invertebr. Pathol. 106:418421.PubMed CrossRef
148. Lin, M.,, A. den Dulk-Ras,, P. J. Hooykaas,, and Y. Rikihisa. 2007. Anaplasma phagocytophilum AnkA secreted by type IV secretion system is tyrosine phosphorylated by Abl-1 to facilitate infection. Cell. Microbiol. 9:26442657.PubMed CrossRef
149. Lin, M.,, and Y. Rikihisa. 2003. Ehrlichia chaffeensis and Anaplasma phagocytophilum lack genes for lipid A biosynthesis and incorporate cholesterol for their survival. Infect. Immun. 71:53245331.PubMed
150. Lin, M.,, and Y. Rikihisa. 2004. Ehrlichia chaffeensis downregulates surface Toll-like receptors 2/4, CD14 and transcription factors PU.1 and inhibits lipopolysaccharide activation of NF-κB, ERK 1/2 and p38 MAPK in host monocytes. Cell. Microbiol. 6:175186.PubMed CrossRef
151. Lin, M.,, C. Zhang,, K. Gibson,, and Y. Rikihisa. 2009. Analysis of complete genome sequence of Neorickettsia risticii: causative agent of Potomac horse fever. Nucleic Acids Res. 37:60766091.PubMed CrossRef
152. Linka, N.,, H. Hurka,, B. F. Lang,, G. Burger,, H. H. Winkler,, C. Stamme,, C. Urbany,, I. Seil,, J. Kusch,, and H. E. Neuhaus. 2003. Phylogenetic relationships of non-mitochondrial nucleotide transport proteins in bacteria and eukaryotes. Gene 306:2735.PubMed
153. Lloyd, S. J.,, S. E. LaPatra,, K. R. Snekvik,, S. St-Hilaire,, K. D. Cain,, and D. R. Call. 2008. Strawberry disease lesions in rainbow trout from southern Idaho are associated with DNA from a Rickettsia-like organism. Dis. Aquat. Organ. 82:111118.PubMed CrossRef
154. Lo, N.,, T. Beninati,, L. Sacchi,, C. Genchi,, and C. Bandi. 2004. Emerging rickettsioses. Parassitologia 46:123126.PubMed
155. Lo, N.,, T. Beninati,, D. Sassera,, E. A. Bouman,, S. Santagati,, L. Gern,, V. Sambri,, T. Masuzawa,, J. S. Gray,, T. G. Jaenson,, A. Bouattour,, M. J. Kenny,, E. S. Guner,, I. G. Kharitonenkov,, I. Bitam,, and C. Bandi. 2006. Widespread distribution and high prevalence of an alpha-proteobacterial symbiont in the tick Ixodes ricinus. Environ. Microbiol. 8:12801287.PubMed CrossRef
156. Lo, N.,, C. Paraskevopoulos,, K. Bourtzis,, S. L. O’Neill,, J. H. Werren,, S. R. Bordenstein,, and C. Bandi. 2007. Taxonomic status of the intracellular bacterium Wolbachia pipientis. Int. J. Syst. Evol. Microbiol. 57:654657.PubMed CrossRef
157. Loy, J. K.,, F. E. Dewhirst,, W. Weber,, P. F. Frelier,, T. L. Garbar,, S. I. Tasca,, and J. W. Templeton. 1996. Molecular phylogeny and in situ detection of the etiologic agent of necrotizing hepatopancreatitis in shrimp. Appl. Environ. Microbiol. 62:34393445.PubMed
158. Maggi, R. G.,, M. Kosoy,, M. Mintzer,, and E. B. Breitschwerdt. 2009. Isolation of Candidatus Bartonella melophagi from human blood. Emerg. Infect. Dis. 15:6668.PubMed CrossRef
159. Malek, J. A.,, J. M. Wierzbowski,, W. Tao,, S. A. Bosak,, D. J. Saranga,, L. Doucette-Stamm,, D. R. Smith,, P. J. McEwan,, and K. J. McKernan. 2004. Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica. Nucleic Acids Res. 32:10591064.PubMed CrossRef
160. Malmstrom, R. R.,, M. T. Cottrell,, H. Elifantz,, and D. L. Kirchman. 2005. Biomass production and assimilation of dissolved organic matter by SAR11 bacteria in the Northwest Atlantic Ocean. Appl. Environ. Microbiol. 71:29792986.PubMed CrossRef
161. Mavromatis, K.,, C. K. Doyle,, A. Lykidis,, N. Ivanova,, M. P. Francino,, P. Chain,, M. Shin,, S. Malfatti,, F. Larimer,, A. Copeland,, J. C. Detter,, M. Land,, P. M. Richardson,, X. J. Yu,, D. H. Walker,, J. W. McBride,, and N. C. Kyrpides. 2006. The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion strategies. J. Bacteriol. 188:40154023.PubMed CrossRef